Comprehensive edge pattern semantic assessment (65 unique patterns)

[turbomam]

Overview

Systematic semantic assessment of all 65 unique edge patterns in kg-microbe transformed data, analyzing subject category + predicate + object category combinations for Biolink Model compliance.

Analysis Date: 2025-11-20 (build from 2025-11-11, commit 77c42d8)

Data Files

• kg_microbe_edge_patterns.tsv - Complete list of patterns with counts by source
• edge_pattern_assessment.md - Detailed semantic assessment of each pattern

Pattern Format

source | subject_category | subject_prefix | predicate | object_category | object_prefix | count

Key Findings

High-Priority Issues (3 patterns, ~239K edges)

1. organism --capable_of--> quality (186,197 edges) → biolink:capable_of used with wrong object type (PhenotypicQuality instead of Occurrent) #438

   • EC codes miscategorized; should be processes not qualities

2. organism --occurs_in--> medium (52,995 edges) → biolink:occurs_in used incorrectly for organism-medium relationships #440

   • Organisms don't occur in media; growth processes do

3. chemical --occurs_in--> assay (340 edges)

   • Wrong direction/predicate; should be assay uses/has_input chemical

Data Quality Issues (~85K edges)

Multiple patterns with (unknown) or (empty) categories:

• METPO nodes missing categories (44,081 edges) → METPO phenotype nodes in madin_etal have missing categories #439
• ENVO environmental nodes (14,888 edges)
• isolation_source nodes (6,775 edges)
• Various NCBITaxon nodes (~2,000 edges)

Node Categorization Issues

• EC enzyme codes: duplicate entries with conflicting categories → EC enzyme codes have duplicate node entries with conflicting categories #437
• CHEBI chemicals categorized as EnvironmentalFeature (910 edges)
• NCBITaxon organisms categorized as EnvironmentalFeature (624 edges)
• PATO qualities used as locations (569 edges)

Non-Standard Predicates (23,289 edges)

• biolink:produces (12,523 edges) - should be has_output
• biolink:associated_with_resistance_to (10,297 edges) - not in Biolink Model
• biolink:is_assessed_by (112 edges) - not in Biolink Model
• biolink:has_chemical_role (357 edges) - may be valid

Valid Patterns (~1.1M edges)

18 patterns are semantically valid including:

• organism --consumes--> chemical (429K edges)
• organism --has_phenotype--> quality (210K edges)
• environment --location_of--> organism (168K edges)
• organism --subclass_of--> organism (173K edges)
• organism --capable_of--> process (6K edges)

Recommendations

Priority 1: Invalid Patterns

1. Fix EC node categories and capable_of usage (biolink:capable_of used with wrong object type (PhenotypicQuality instead of Occurrent) #438)
2. Fix organism-medium relationship (biolink:occurs_in used incorrectly for organism-medium relationships #440)
3. Reverse chemical-assay relationship

Priority 2: Data Quality

1. Assign missing categories (METPO phenotype nodes in madin_etal have missing categories #439)
2. Review misclassified nodes
3. Fix PATO-as-location patterns

Priority 3: Standardization

1. Map produces to has_output
2. Request associated_with_resistance_to in Biolink Model
3. Review non-standard predicates

Methodology

Assessment based on:

• Biolink Model predicate definitions and constraints
• Semantic appropriateness of subject-predicate-object combinations
• Standard usage patterns in biomedical knowledge graphs
• Domain knowledge of microbiology and biological processes

Related Issues

• EC enzyme codes have duplicate node entries with conflicting categories #437 - EC enzyme code duplicate categories
• biolink:capable_of used with wrong object type (PhenotypicQuality instead of Occurrent) #438 - capable_of predicate range violation
• METPO phenotype nodes in madin_etal have missing categories #439 - Missing METPO categories
• biolink:occurs_in used incorrectly for organism-medium relationships #440 - occurs_in semantic violation
• Sphinx sources addition #30 - Broader KGX format compliance

Files

See attached analysis files in metpo repository for complete assessment details.

[turbomam]

kg_microbe_edge_patterns.tsv